User: Travis

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Travis0
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Posts by Travis

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How to process Plink2 --score across chromosomes
... I'd like to run the --score flag across chromosomes. I tried this syntax: # PBS -t 1-22 plink2 --pfile data.chr${PBS_ARRAYID} --score snps_file header list-variants --memory 4500 --threads 5 This generated only one set of output files (.sscore, sscore.vars, and .log), ostensibly from ch ...
plink2 written 7 days ago by Travis0 • updated 7 days ago by chrchang5234.6k
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Answer: A: Error: --score takes at most three numeric parameters.
... The modifiers 'sum' and 'no-mean-imputation' are mutually exclusive according to the documentation. ...
written 10 days ago by Travis0
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Error: --score takes at most three numeric parameters.
... I used the --score flag to calculate a polygenic risk score from dosage data. The arguments "1 2 3" are the columns for SNP ID, risk allele, and the absolute value of beta for the risk allele, respectively. These are the only columns in the file snp_list. My script is: plink2 \ --pfile mydata \ ...
plink2 written 10 days ago by Travis0 • updated 10 days ago by chrchang5234.6k
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PLINK dosage data - convert and/or read in R
... I have PLINK dosage files in the form pgen/psam/pvar. I would like to know how to do either/both of the following: 1. Convert the file set to bed/bim/fam files (hard-calls) 2. Read the allele dosage from pgen into R as a continuous variable Thanks. ...
plink written 11 days ago by Travis0 • updated 10 days ago by chrchang5234.6k

Latest awards to Travis

Scholar 10 days ago, created an answer that has been accepted. For A: Error: --score takes at most three numeric parameters.

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